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r1647
File Last Change
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pisa/ 1635 (9 years ago) by jmduarteg: Fixed pisa oligomeric prediction behaviour when mixed assembly sizes in same assembly group
CSAConnection.java 1392 (11 years ago) by jmduarteg: MAJOR CHANGE: now able to read and treat properly HETATMS and nucleotides from PDB entries. All tests pass. Anyway surely there will be some bugs to iron out still.
ECConnection.java 1372 (11 years ago) by jmduarteg: MAJOR INTERFACE CHANGE: the main PDB data loading interface has changed. Now all loading of data occurs through PdbAsymUnit. Refactoring of some classes: Pdb is now PdbChain.
EmblWSDBfetchConnection.java 1507 (10 years ago) by jmduarteg: Now supporting both uniprot and uniparc entries in HomologList
GTGHit.java 1372 (11 years ago) by jmduarteg: MAJOR INTERFACE CHANGE: the main PDB data loading interface has changed. Now all loading of data occurs through PdbAsymUnit. Refactoring of some classes: Pdb is now PdbChain.
GTGHitList.java 1326 (11 years ago) by jmduarteg: Renamed xxxxError classes to xxxxException as they should be.
GTGParser.java 1326 (11 years ago) by jmduarteg: Renamed xxxxError classes to xxxxException as they should be.
JPredConnection.java 1370 (11 years ago) by hstehr: Updated some JavaDocs
JPredProgressRetriever.java 1060 (12 years ago) by hstehr: New helper classes JPredProgressRetriever and JPredNotifier which can be used to run JPredConnection in a thread and notify some GUI component of the progress.
JPredStopNotifier.java 1060 (12 years ago) by hstehr: New helper classes JPredProgressRetriever and JPredNotifier which can be used to run JPredConnection in a thread and notify some GUI component of the progress.
NoMatchFoundException.java 1040 (12 years ago) by jmduarteg: New UniprotConnection taken from Henning's structural impact project (lots of new jar dependencies with that). New EmblWSDBFetchConnection class to get sequences from EMBL web services.
PDomainsConnection.java 1347 (11 years ago) by hstehr: moving project CCCP to this repository
PhosphoSiteConnection.java 1231 (11 years ago) by hstehr: Adding class PhosphoSiteConnection
PiqsiAnnotation.java 1598 (9 years ago) by jmduarteg: New classes to parse PiQSi annotation file
PiqsiConnection.java 1598 (9 years ago) by jmduarteg: New classes to parse PiQSi annotation file
PrositeHit.java 1009 (12 years ago) by hstehr: refactoring: moved many many classes to more appropriate packages; created new packages owl.core.sequence.alignment, owl.core.structure.alignment, owl.core.structure.features
PrositeScanner.java 1009 (12 years ago) by hstehr: refactoring: moved many many classes to more appropriate packages; created new packages owl.core.sequence.alignment, owl.core.structure.alignment, owl.core.structure.features
ScopConnection.java 1472 (10 years ago) by jmduarteg: Fixed a couple of problems with ScopConnection. Added another atom type.
SiftsConnection.java 1637 (9 years ago) by jmduarteg: Minor javadoc improvement
UniProtConnection.java 1535 (10 years ago) by jmduarteg: Restructured how the UniprotConnection is used. Now all uniprot connection stuff done within the class
UniProtPdbRef.java 1347 (11 years ago) by hstehr: moving project CCCP to this repository
UniprotLocalConnection.java 1642 (8 years ago) by jmduarteg: Now both taxonomy and uniprot tables are read from same database
UnirefXMLParser.java 1557 (10 years ago) by jmduarteg: Fixed bug: for a uniref100 cluster member, was taking the representative's uniprot id/tax id instead of the member's. Database was not correctly modelled -> need also the tax ids for cluster members (and then to query the tax ids from members and not from representative)
package-info.java 1005 (12 years ago) by hstehr: refactoring: renaming proteinstructure to structure and tools to util; moving connections,features,runners,sequence,structure,util to owl.core
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